Then, in the base folder of your book or article, create a symbolic link to the real BibDesk database file:

ln -s ~/Documents/BibDesk/Database/References.bib BibRef.bib

The “base folder” is the folder where your .scriv file is. Scrivener creates the .tex files in a subfolder, so that’s why you need the “..” before “BibRef” above. By the way, I called the link “BibRef” just to make it clearly different from the actual database name, but you can use anything you like. As long as it doesn’t contain blanks or strange symbols.